## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Combine all ORF counting methods

Now we combine the TSS-only, the TES-only and the TSS.TES methods for all 5 normalization methods

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only)

TSS only

Only those reads were counted, where LoRTIA

found the 5-prime adapters!

## Error in fread(paste0(fig.dir, ".norm_host", "/", norm.method, "_", EndType,  : 
##   File 'LoRTIA_virus/TSS_abund.norm_host/host_read.count_TSS_abund.mean.tsv' does not exist or is non-readable. getwd()=='C:/GitHub/EHV-1-dynamic'
## Error in fread(paste0(fig.dir, ".norm_VST", "/", norm.method, "_", EndType,  : 
##   File 'LoRTIA_virus/TSS_abund.norm_VST/VST_TSS_abund.mean.tsv' does not exist or is non-readable. getwd()=='C:/GitHub/EHV-1-dynamic'

TES only

Only those reads were counted, where LoRTIA

found the 3-prime adapters!

## Error in fread(paste0(fig.dir, ".norm_host", "/", norm.method, "_", EndType,  : 
##   File 'LoRTIA_virus/TES_abund.norm_host/host_read.count_TES_abund.mean.tsv' does not exist or is non-readable. getwd()=='C:/GitHub/EHV-1-dynamic'
## Error in fread(paste0(fig.dir, ".norm_VST", "/", norm.method, "_", EndType,  : 
##   File 'LoRTIA_virus/TES_abund.norm_VST/VST_TES_abund.mean.tsv' does not exist or is non-readable. getwd()=='C:/GitHub/EHV-1-dynamic'

TSS.TES

Only those reads were counted, where LoRTIA

found both 5-prime AND 3-prime adapters!

## Error in fread(paste0(fig.dir, ".norm_host", "/", norm.method, "_", EndType,  : 
##   File 'LoRTIA_virus/TSS.TES_abund.norm_host/host_read.count_TSS.TES_abund.mean.tsv' does not exist or is non-readable. getwd()=='C:/GitHub/EHV-1-dynamic'

Combine dynamics

Gene dynamics, according to literature-based kinetic classes

## [1] TRUE
## [1] "ORF1"

Mean and SD with linear connection

Mean and SD with loess function

Barplots

Dotplots

Combined dynamics of kinetic classes/clusters

De Novo - Significant

De Novo - All clusters

Literature clusters

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Gene-pair ratios

These pairs were analyzed: ie180/us1, ie180/ep0, us1/ep0, noir1/noir2, noir1/ie180, noir2/ie180